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• Water and energy input in crop production as a basis for agricultural development. • Irrigation water and fertilisers are important factors in generating CO 2 emissions. • Optimization model for sustainable agricultural development is established. • Agricultural resources utilization efficiency is improved. Agricultural sustainability is substantially influenced by the water-energy-food (WEF) nexus and CO 2 emissions. However, previous research has minimally focused on the impacts of agricultural CO 2 emissions on sustainable agricultural management. Therefore, to address this research gap, based on the water-energy-food nexus index (WEFNI) and CO 2 emissions, this study constructs a multi-objective nonlinear optimisation method for sustainable agricultural management. The crop production and emissions reduction potential under various optimisation schemes were analysed using the major crops (rice, wheat, maize, and cotton) in the Tarim River Basin (TRB), the largest inland river in China, as a test case.Cotton, as a high water- and energy-consuming crop, had a lower water and energy mass productivity than other crops. Improvements in irrigation efficiency and mechanisation in the TRB have had major effects on water conversation and carbon reduction. The intensity of agricultural CO 2 emissions in the basin showed a decreasing trend from 1990 to 2020, with wheat CO 2 emissions decreasing only slightly (-10860.92 kg CO 2 eq/ha). In the optimal scenario that ensures maximum WEFNI and minimum agricultural CO 2 emissions, the irrigation efficiency increases to 0.59, and the crop area for wheat and maize increases substantially, indicating that the TRB still exhibits potential for crop production. Most importantly, the Dina would save 4250.52 × 104 m3 of water resources, increase the area of maize cultivation by 1249.84 ha, increase food production by 0.68 × 104 tonnes, and reduce energy consumption and agricultural CO 2 emissions by 1297.52 × 104 MJ and 890.25 × 104 kg CO 2 eq, respectively. The optimisation model had obvious effects on water saving and agricultural CO 2 reduction and may represent a vital component in completing the "14th Five-Year Plan" of the basin and promoting the sustainable agricultural development. [ABSTRACT FROM AUTHOR]